Kabupaten Natuna history can not be separated from the Riau Islands regency history, as before as the self-autonomy, Natuna Regency is the area Kepualauan and Riau.

Based on a decree from the Delegation of the Republic of Indonesia, Central Sumatra Province on 18 May 1956 to merge themselves in the Region of the Republic of Indonesia, Riau Islands and given the status of Regional Autonomy Level II as head of the Regent are areas supervise 4 kewedanaan as follows:

Seven Island Kewedanaan supervise the District Jemaja, Siantan, Midai, Serasan, Tambelan, Bunguran West and East Bunguran with kewedanaan laiannya removed based on a decree from the Governor of the Head of Regional Level I Riau on 9 August 1964 No. UP/247/5/1965. Based on these provisions, as of 1 January 1966 all local administrative kewedanaan in the Riau Islands regency deleted.

Natuna Regency was formed based on Law No. 53 of 1999 results of the District of Riau Islands, which consist of the District 6 District Bunguran East, West Bunguran, Jemaja, Siantan, Midai, and Serasan and one Assistant District Tebang Ladan.

Along with the authority of regional autonomy, Kabupaten Natuna area and conduct of the district, which until 2004 to 10 districts with the addition, District Palmatak, Subi, Bunguran North, and Sea Island to the number of villages / village of 53.

Until the year 2007, the Kabupaten Natuna has 16 District. District 6 of the new District is among the three islands, Bunguran Northeast, Central Bunguran, Siantan South, East and Siantan East Jemaja the total number of villages / village of 75.

However, after discharge law - Act No. 33 of 2008 on The Regency Anambas Islands on 21 July 2008 where some of the District, among other Siantan District, Central District Siantan, Siantan South District, District Palmatak, Jemaja District and Eastern District Jemaja incoming administration in the region Anambas Islands District, and at the time This local administration in the Sub District, lies only 12 District.